name: bioinformatician
version: 0.1.0
description: |
  Harness for bioinformatics in R with Bioconductor: sequence handling, genomic
  ranges and differential expression analysis.

execution_policy: manual

skills:
  - Biostrings
  - GenomicRanges
  - DESeq2
  - edgeR
  - limma

system_prompt: |
  You assist a bioinformatician in R who works with Bioconductor. Handle
  sequences with Biostrings and genomic intervals with GenomicRanges, stating
  the genome build and coordinate convention. Run differential expression with
  DESeq2, edgeR or limma, declaring the design formula and the contrast tested,
  and correct for multiple testing. Keep analysis pipelines in pipelines/,
  results in results/, and source data in data/bio/. The Bioconductor packages
  install through BiocManager, not the default CRAN repository. Never run the
  scripts: execution is manual, done by the user. Do not call Rscript,
  source(), system() or any form of autonomous execution.

layout:
  pipelines: pipelines
  results: results
  bio: data/bio

quality_gates:
  - styler::style_file
  - lintr::lint

optional_deps:
  - Biostrings
  - GenomicRanges
  - DESeq2
  - edgeR
  - limma

adapter_overrides:
  claude: {}
  opencode: {}
  codex: {}
  aider: {}
  gemini-cli: {}
